西藏纳木错湖芯正构烷烃及其反映的8.4 ka以来的环境变化

采用索氏抽提法提取纳木错NMLC-1孔湖芯沉积物中的正构烷烃, 利用GC/MS进行了测试. 在已经建立的深度-年代曲线基础上, 通过分析正构烷烃的组成与含量, 结合TOC, TN和CaCO₃等环境代用指标, 重建了纳木错湖区约8.4 ka以来的环境变化历史. 结果表明: 约8.4~6.7 ka BP期间, 环境较温暖, 降水呈增加趋势, 末期变冷干. 约6.7~2.9 ka BP期间可分为两个亚期, 早期温暖湿润, 至6.0 ka BP左右达到环境最适宜期; 晚期温度波动降低, 陆生植被和沉水植物退化, 以3.0 ka BP左右的冷事件结束. 约2.9 ka BP~现在, 冷暖交替, 1.4 ka BP左右开始趋于干燥, 600~400 a BP间的降温体现了小冰期特征.     

Following the signal sequence from ribosomal tunnel exit to signal recognition particle

Membrane and secretory proteins can be co-translationally inserted into or translocated across the membrane. This process is dependent on signal sequence recognition on the ribosome by the signal recognition particle (SRP), which results in targeting of the ribosome-nascent-chain complex to the protein-conducting channel at the membrane. Here we present an ensemble of structures at subnanometre resolution, revealing the signal sequence both at the ribosomal tunnel exit and in the bacterial and eukaryotic ribosome-SRP complexes. Molecular details of signal sequence interaction in both prokaryotic and eukaryotic complexes were obtained by fitting high-resolution molecular models. The signal sequence is presented at the ribosomal tunnel exit in an exposed position ready for accommodation in the hydrophobic groove of the rearranged SRP54 M domain. Upon ribosome binding, the SRP54 NG domain also undergoes a conformational rearrangement, priming it for the subsequent docking reaction with the NG domain of the SRP receptor. These findings provide the structural basis for improving our understanding of the early steps of co-translational protein sorting.     

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints.     

Proteome survey reveals modularity of the yeast cell machinery

Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. Here we report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry. Through systematic tagging of open reading frames (ORFs), the majority of complexes were purified several times, suggesting screen saturation. The richness of the data set enabled a de novo characterization of the composition and organization of the cellular machinery. The ensemble of cellular proteins partitions into 491 complexes, of which 257 are novel, that differentially combine with additional attachment proteins or protein modules to enable a diversification of potential functions. Support for this modular organization of the proteome comes from integration with available data on expression, localization, function, evolutionary conservation, protein structure and binary interactions. This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling.     

Evidence of power-law flow in the Mojave desert mantle

Studies of the Earth's response to large earthquakes can be viewed as large rock deformation experiments in which sudden stress changes induce viscous flow in the lower crust and upper mantle that lead to observable postseismic surface deformation. Laboratory experiments suggest that viscous flow of deforming hot lithospheric rocks is characterized by a power law in which strain rate is proportional to stress raised to a power, n (refs 2, 3). Most geodynamic models of flow in the lower crust and upper mantle, however, resort to newtonian (linear) stress-strain rate relations. Here we show that a power-law model of viscous flow in the mantle with n = 3.5 successfully explains the spatial and temporal evolution of transient surface deformation following the 1992 Landers and 1999 Hector Mine earthquakes in southern California. A power-law rheology implies that viscosity varies spatially with stress causing localization of strain, and varies temporally as stress evolves, rendering newtonian models untenable. Our findings are consistent with laboratory-derived flow law parameters for hot and wet olivine--the most abundant mineral in the upper mantle--and support the contention that, at least beneath the Mojave desert, the upper mantle is weaker than the lower crust.     

Chymotrypsin C (CTRC) variants that diminish activity or secretion are associated with chronic pancreatitis

Chronic pancreatitis is a persistent inflammatory disease of the pancreas, in which the digestive protease trypsin has a fundamental pathogenetic role. Here we have analyzed the gene encoding the trypsin-degrading enzyme chymotrypsin C (CTRC) in German subjects with idiopathic or hereditary chronic pancreatitis. Two alterations in this gene, p.R254W and p.K247_R254del, were significantly overrepresented in the pancreatitis group, being present in 30 of 901 (3.3%) affected individuals but only 21 of 2,804 (0.7%) controls (odds ratio (OR) = 4.6; confidence interval (CI) = 2.6-8.0; P = 1.3 x 10(-7)). A replication study identified these two variants in 10 of 348 (2.9%) individuals with alcoholic chronic pancreatitis but only 3 of 432 (0.7%) subjects with alcoholic liver disease (OR = 4.2; CI = 1.2-15.5; P = 0.02). CTRC variants were also found in 10 of 71 (14.1%) Indian subjects with tropical pancreatitis but only 1 of 84 (1.2%) healthy controls (OR = 13.6; CI = 1.7-109.2; P = 0.0028). Functional analysis of the CTRC variants showed impaired activity and/or reduced secretion. The results indicate that loss-of-function alterations in CTRC predispose to pancreatitis by diminishing its protective trypsin-degrading activity.     

Analytic and Dynamic Approach to Collaboration: A Transdisciplinary Case Study on Sustainable Landscape Development in a Swiss Prealpine Region

The involvement of stakeholders and the public in societal decision processes has lately received increased attention. We suggest that appropriate and tailored techniques should be selected and integrated to provide the prerequisites for inclusive involvement depending on the issue, type, goals and phase of the decision process in question, i.e. an analytic, systematic and dynamic approach to collaboration. In a transdisciplinary case study design we integrate diverse analytical methods whereby a process of mutual learning between science and people from outside academia is strived for. Our framework for collaboration is illustrated by a case study on sustainable landscape development in the Swiss prealpine region of Appenzell Ausserrhoden.

Mesoscale conformational changes in the DNA-repair complex Rad50/Mre11/Nbs1 upon binding DNA

The human Rad50/Mre11/Nbs1 complex (hR/M/N) functions as an essential guardian of genome integrity by directing the proper processing of DNA ends, including DNA breaks. This biological function results from its ability to tether broken DNA molecules. hR/M/N's dynamic molecular architecture consists of a globular DNA-binding domain from which two 50-nm-long coiled coils protrude. The coiled coils are flexible and their apices can self-associate. The flexibility of the coiled coils allows their apices to adopt an orientation favourable for interaction. However, this also allows interaction between the tips of two coiled coils within the same complex, which competes with and frustrates the intercomplex interaction required for DNA tethering. Here we show that the dynamic architecture of hR/M/N is markedly affected by DNA binding. DNA binding by the hR/M/N globular domain leads to parallel orientation of the coiled coils; this prevents intracomplex interactions and favours intercomplex associations needed for DNA tethering. The hR/M/N complex thus is an example of a biological nanomachine in which binding to its ligand, in this case DNA, affects the functional conformation of a domain located 50 nm distant.